Starting phenix.real_space_refine (version: dev) on Mon Apr 4 22:50:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbw_13307/04_2022/7pbw_13307_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9500 Number of models: 1 Model: "" Number of chains: 54 Chain: "AA" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 372 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BB" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BC" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BD" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BE" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BF" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BG" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BH" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BI" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 353 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "AA" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 222 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AB" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AC" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AD" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 222 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AE" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AF" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AG" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AH" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'BCL': 2, '7OT': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BA" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BB" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BC" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BD" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'BCL': 1, 'LDA': 1, ' CA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BE" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BF" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BH" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BI" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 99 Unusual residues: {'BCL': 1, 'LDA': 2, ' CA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AA" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "AB" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AC" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AD" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "AE" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AF" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "AG" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "AH" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "AI" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BA" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "BB" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "BC" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "BD" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BE" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BF" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "BG" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "BH" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "BI" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 5.78, per 1000 atoms: 0.61 Number of scatterers: 9500 At special positions: 0 Unit cell: (87.12, 87.12, 77.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 9 19.99 S 18 16.00 Mg 27 11.99 O 1562 8.00 N 1206 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=27, symmetry=0 Number of additional bonds: simple=27, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 985.2 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 9 Processing helix chain 'AA' and resid 12 through 37 Proline residue: AA 17 - end of helix Processing helix chain 'AA' and resid 39 through 49 removed outlier: 6.210A pdb=" N SERAA 48 " --> pdb=" O TYRAA 44 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALAAA 49 " --> pdb=" O TYRAA 45 " (cutoff:3.500A) Processing helix chain 'AB' and resid 4 through 9 Processing helix chain 'AB' and resid 12 through 37 Proline residue: AB 17 - end of helix Processing helix chain 'AB' and resid 40 through 49 removed outlier: 6.246A pdb=" N SERAB 48 " --> pdb=" O TYRAB 44 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALAAB 49 " --> pdb=" O TYRAB 45 " (cutoff:3.500A) Processing helix chain 'AC' and resid 4 through 9 Processing helix chain 'AC' and resid 12 through 37 Proline residue: AC 17 - end of helix Processing helix chain 'AC' and resid 40 through 49 removed outlier: 6.215A pdb=" N SERAC 48 " --> pdb=" O TYRAC 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALAAC 49 " --> pdb=" O TYRAC 45 " (cutoff:3.500A) Processing helix chain 'AD' and resid 4 through 9 Processing helix chain 'AD' and resid 12 through 37 Proline residue: AD 17 - end of helix Processing helix chain 'AD' and resid 40 through 49 removed outlier: 6.252A pdb=" N SERAD 48 " --> pdb=" O TYRAD 44 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALAAD 49 " --> pdb=" O TYRAD 45 " (cutoff:3.500A) Processing helix chain 'AE' and resid 4 through 9 Processing helix chain 'AE' and resid 12 through 37 Proline residue: AE 17 - end of helix Processing helix chain 'AE' and resid 40 through 49 removed outlier: 6.238A pdb=" N SERAE 48 " --> pdb=" O TYRAE 44 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALAAE 49 " --> pdb=" O TYRAE 45 " (cutoff:3.500A) Processing helix chain 'AF' and resid 4 through 9 Processing helix chain 'AF' and resid 12 through 37 Proline residue: AF 17 - end of helix Processing helix chain 'AF' and resid 40 through 49 removed outlier: 6.233A pdb=" N SERAF 48 " --> pdb=" O TYRAF 44 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALAAF 49 " --> pdb=" O TYRAF 45 " (cutoff:3.500A) Processing helix chain 'AG' and resid 4 through 9 Processing helix chain 'AG' and resid 12 through 37 Proline residue: AG 17 - end of helix Processing helix chain 'AG' and resid 40 through 49 removed outlier: 6.201A pdb=" N SERAG 48 " --> pdb=" O TYRAG 44 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALAAG 49 " --> pdb=" O TYRAG 45 " (cutoff:3.500A) Processing helix chain 'AH' and resid 4 through 9 Processing helix chain 'AH' and resid 12 through 37 Proline residue: AH 17 - end of helix Processing helix chain 'AH' and resid 40 through 49 removed outlier: 6.243A pdb=" N SERAH 48 " --> pdb=" O TYRAH 44 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALAAH 49 " --> pdb=" O TYRAH 45 " (cutoff:3.500A) Processing helix chain 'AI' and resid 4 through 9 Processing helix chain 'AI' and resid 12 through 37 Proline residue: AI 17 - end of helix Processing helix chain 'AI' and resid 40 through 49 removed outlier: 6.243A pdb=" N SERAI 48 " --> pdb=" O TYRAI 44 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALAAI 49 " --> pdb=" O TYRAI 45 " (cutoff:3.500A) Processing helix chain 'BA' and resid 15 through 46 Processing helix chain 'BB' and resid 15 through 46 Processing helix chain 'BC' and resid 15 through 46 Processing helix chain 'BD' and resid 15 through 46 Processing helix chain 'BE' and resid 15 through 46 Processing helix chain 'BF' and resid 15 through 46 Processing helix chain 'BG' and resid 15 through 46 Processing helix chain 'BH' and resid 15 through 46 Processing helix chain 'BI' and resid 15 through 46 487 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 2507 1.37 - 1.57: 6952 1.57 - 1.78: 9 1.78 - 1.98: 27 1.98 - 2.19: 108 Bond restraints: 9603 Sorted by residual: bond pdb=" C23 7OTAB 103 " pdb=" C25 7OTAB 103 " ideal model delta sigma weight residual 1.583 1.451 0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C23 7OTAA 103 " pdb=" C25 7OTAA 103 " ideal model delta sigma weight residual 1.583 1.451 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C23 7OTAF 103 " pdb=" C25 7OTAF 103 " ideal model delta sigma weight residual 1.583 1.451 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C23 7OTAG 103 " pdb=" C25 7OTAG 103 " ideal model delta sigma weight residual 1.583 1.451 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C23 7OTAD 103 " pdb=" C25 7OTAD 103 " ideal model delta sigma weight residual 1.583 1.451 0.132 2.00e-02 2.50e+03 4.35e+01 ... (remaining 9598 not shown) Histogram of bond angle deviations from ideal: 84.93 - 99.93: 108 99.93 - 114.93: 6511 114.93 - 129.93: 6386 129.93 - 144.92: 279 144.92 - 159.92: 81 Bond angle restraints: 13365 Sorted by residual: angle pdb=" C24 7OTAC 103 " pdb=" C23 7OTAC 103 " pdb=" C25 7OTAC 103 " ideal model delta sigma weight residual 68.21 117.99 -49.78 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C24 7OTAG 103 " pdb=" C23 7OTAG 103 " pdb=" C25 7OTAG 103 " ideal model delta sigma weight residual 68.21 117.99 -49.78 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C24 7OTAH 103 " pdb=" C23 7OTAH 103 " pdb=" C25 7OTAH 103 " ideal model delta sigma weight residual 68.21 117.99 -49.78 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C24 7OTAE 103 " pdb=" C23 7OTAE 103 " pdb=" C25 7OTAE 103 " ideal model delta sigma weight residual 68.21 117.98 -49.77 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C24 7OTAI 103 " pdb=" C23 7OTAI 103 " pdb=" C25 7OTAI 103 " ideal model delta sigma weight residual 68.21 117.97 -49.76 3.00e+00 1.11e-01 2.75e+02 ... (remaining 13360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4378 17.10 - 34.20: 407 34.20 - 51.30: 74 51.30 - 68.40: 39 68.40 - 85.50: 52 Dihedral angle restraints: 4950 sinusoidal: 2475 harmonic: 2475 Sorted by residual: dihedral pdb=" C3 BCLAA 102 " pdb=" C5 BCLAA 102 " pdb=" C6 BCLAA 102 " pdb=" C7 BCLAA 102 " ideal model delta sinusoidal sigma weight residual -60.00 -97.58 37.58 3 9.00e+00 1.23e-02 1.83e+01 dihedral pdb=" CA LEUBE 13 " pdb=" C LEUBE 13 " pdb=" N THRBE 14 " pdb=" CA THRBE 14 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEUBC 13 " pdb=" C LEUBC 13 " pdb=" N THRBC 14 " pdb=" CA THRBC 14 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 750 0.028 - 0.056: 371 0.056 - 0.085: 96 0.085 - 0.113: 78 0.113 - 0.141: 64 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA LEUBB 50 " pdb=" N LEUBB 50 " pdb=" C LEUBB 50 " pdb=" CB LEUBB 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA LEUBF 50 " pdb=" N LEUBF 50 " pdb=" C LEUBF 50 " pdb=" CB LEUBF 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA LEUBH 50 " pdb=" N LEUBH 50 " pdb=" C LEUBH 50 " pdb=" CB LEUBH 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1356 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCLAH 102 " -0.038 1.50e-02 4.44e+03 3.38e-02 2.54e+01 pdb=" C2 BCLAH 102 " 0.039 1.50e-02 4.44e+03 pdb=" C3 BCLAH 102 " 0.036 1.50e-02 4.44e+03 pdb=" C4 BCLAH 102 " 0.001 1.50e-02 4.44e+03 pdb=" C5 BCLAH 102 " -0.038 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAF 102 " -0.038 1.50e-02 4.44e+03 3.30e-02 2.41e+01 pdb=" C2 BCLAF 102 " 0.045 1.50e-02 4.44e+03 pdb=" C3 BCLAF 102 " 0.028 1.50e-02 4.44e+03 pdb=" C4 BCLAF 102 " 0.001 1.50e-02 4.44e+03 pdb=" C5 BCLAF 102 " -0.035 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCLAH 102 " -0.061 3.00e-02 1.11e+03 5.32e-02 1.57e+01 pdb=" CBA BCLAH 102 " -0.059 3.00e-02 1.11e+03 pdb=" CGA BCLAH 102 " 0.057 3.00e-02 1.11e+03 pdb=" O1A BCLAH 102 " 0.001 3.00e-02 1.11e+03 pdb=" O2A BCLAH 102 " 0.062 3.00e-02 1.11e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1475 2.77 - 3.31: 8491 3.31 - 3.84: 18068 3.84 - 4.37: 22120 4.37 - 4.90: 35220 Nonbonded interactions: 85374 Sorted by model distance: nonbonded pdb=" O GLYBG 51 " pdb="CA CABG 102 " model vdw 2.243 2.510 nonbonded pdb=" O GLYBB 51 " pdb="CA CABB 102 " model vdw 2.247 2.510 nonbonded pdb=" O GLYBC 51 " pdb="CA CABC 102 " model vdw 2.251 2.510 nonbonded pdb=" O GLYBH 51 " pdb="CA CABH 102 " model vdw 2.254 2.510 nonbonded pdb=" OXT GLYBD 51 " pdb="CA CABD 102 " model vdw 2.255 2.510 ... (remaining 85369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AB' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AC' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AD' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AE' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AF' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AG' and (resid 1 through 50 or resid 101 through 104)) selection = (chain 'AH' and (resid 1 through 50 or resid 101 through 104)) selection = chain 'AI' } ncs_group { reference = (chain 'BA' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BB' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BC' and (resid 5 through 51 or resid 101 through 103)) selection = chain 'BD' selection = (chain 'BE' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BF' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BG' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BH' and (resid 5 through 51 or resid 101 through 103)) selection = (chain 'BI' and (resid 5 through 51 or resid 101 through 103)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 9 9.91 5 Mg 27 5.21 5 S 18 5.16 5 C 6678 2.51 5 N 1206 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.450 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 28.520 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.015 0.132 9603 Z= 0.704 Angle : 4.320 49.780 13365 Z= 1.466 Chirality : 0.046 0.141 1359 Planarity : 0.009 0.053 1530 Dihedral : 16.893 85.500 3348 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.25), residues: 828 helix: 2.72 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.69 (0.37), residues: 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.913 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 1.8413 time to fit residues: 175.8274 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 9603 Z= 0.282 Angle : 2.418 23.800 13365 Z= 0.829 Chirality : 0.044 0.123 1359 Planarity : 0.006 0.037 1530 Dihedral : 18.636 89.245 2088 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.25), residues: 828 helix: 3.76 (0.17), residues: 567 sheet: None (None), residues: 0 loop : 0.66 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.898 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 1.8208 time to fit residues: 151.3317 Evaluate side-chains 78 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 9603 Z= 0.253 Angle : 2.378 23.333 13365 Z= 0.813 Chirality : 0.043 0.119 1359 Planarity : 0.006 0.039 1530 Dihedral : 18.268 88.927 2088 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.24), residues: 828 helix: 3.90 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.46 (0.32), residues: 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.933 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 79 average time/residue: 1.8024 time to fit residues: 149.7575 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.4423 time to fit residues: 2.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 9603 Z= 0.224 Angle : 2.339 24.387 13365 Z= 0.799 Chirality : 0.042 0.118 1359 Planarity : 0.005 0.040 1530 Dihedral : 17.137 86.682 2088 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.24), residues: 828 helix: 3.98 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.41 (0.32), residues: 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.910 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 1.8686 time to fit residues: 155.0724 Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.6912 time to fit residues: 4.5587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 9603 Z= 0.230 Angle : 2.355 24.353 13365 Z= 0.804 Chirality : 0.042 0.118 1359 Planarity : 0.005 0.040 1530 Dihedral : 17.010 86.064 2088 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.24), residues: 828 helix: 3.99 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.31 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.922 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 1.8024 time to fit residues: 149.7782 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.5664 time to fit residues: 2.6881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 9603 Z= 0.230 Angle : 2.352 24.097 13365 Z= 0.803 Chirality : 0.042 0.118 1359 Planarity : 0.005 0.040 1530 Dihedral : 16.733 86.245 2088 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.24), residues: 828 helix: 3.99 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.31 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.890 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 1.8089 time to fit residues: 150.1853 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.6167 time to fit residues: 2.6875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 9603 Z= 0.168 Angle : 2.283 23.552 13365 Z= 0.776 Chirality : 0.039 0.113 1359 Planarity : 0.005 0.038 1530 Dihedral : 15.502 86.674 2088 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.74 (0.25), residues: 828 helix: 4.24 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.48 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.916 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 1.8260 time to fit residues: 151.7269 Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.6322 time to fit residues: 2.7304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 9603 Z= 0.181 Angle : 2.296 23.885 13365 Z= 0.781 Chirality : 0.040 0.114 1359 Planarity : 0.005 0.037 1530 Dihedral : 15.477 87.221 2088 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.67 (0.24), residues: 828 helix: 4.17 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.50 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.987 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 1.7878 time to fit residues: 148.6512 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.0000 chunk 22 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 9603 Z= 0.155 Angle : 2.263 23.491 13365 Z= 0.768 Chirality : 0.038 0.111 1359 Planarity : 0.005 0.036 1530 Dihedral : 14.737 88.638 2088 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.25), residues: 828 helix: 4.27 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.68 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.933 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 1.8284 time to fit residues: 153.9740 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 9603 Z= 0.250 Angle : 2.326 25.380 13365 Z= 0.795 Chirality : 0.043 0.121 1359 Planarity : 0.005 0.036 1530 Dihedral : 16.135 86.268 2088 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.50 (0.24), residues: 828 helix: 4.03 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.49 (0.33), residues: 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.893 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 1.7798 time to fit residues: 147.8757 Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.116363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.098648 restraints weight = 6675.699| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 0.57 r_work: 0.2888 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.2822 rms_B_bonded: 1.16 restraints_weight: 0.1250 r_work: 0.2763 rms_B_bonded: 1.76 restraints_weight: 0.0625 r_work: 0.2672 rms_B_bonded: 2.84 restraints_weight: 0.0312 r_work: 0.2528 rms_B_bonded: 4.99 restraints_weight: 0.0156 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 9603 Z= 0.261 Angle : 2.355 26.324 13365 Z= 0.805 Chirality : 0.043 0.121 1359 Planarity : 0.006 0.038 1530 Dihedral : 17.172 86.445 2088 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.33 (0.24), residues: 828 helix: 3.91 (0.16), residues: 567 sheet: None (None), residues: 0 loop : 0.37 (0.33), residues: 261 =============================================================================== Job complete usr+sys time: 2817.03 seconds wall clock time: 51 minutes 4.39 seconds (3064.39 seconds total)